Simulate a single tree sequence from the given inference setup

Simulates a tree sequence object from a model with parameters as specified either by sampling from priors or by a given list of fixed parameter values

simulate_model(
  model,
  parameters,
  sequence_length,
  recombination_rate,
  mutation_rate = 0,
  data = NULL,
  format = c("ts", "files"),
  engine = NULL,
  model_args = NULL,
  engine_args = NULL,
  attempts = 1000
)

Arguments

model: Either a slendr model generating function (in which case engine must be either "msprime" or "slim", i.e. one of the two of slendr's simulation back ends), or a path to a custom user-defined SLiM or msprime script (in which case engine must be "files").
parameters: A list of prior distributions to use for sampling of model parameters
sequence_length: Amount of sequence to simulate using slendr (in base pairs). Ignored when custom simulations scripts are provided.
recombination_rate: Recombination rate to use for the simulation Ignored when custom simulations scripts are provided.
mutation_rate: Mutation rate to use for the simulation Ignored when custom simulations scripts are provided.
engine: Which simulation engine to use? Values "msprime" and "slim" will use one of the built-in slendr simulation back ends. Which engine will be used is determined by the nature of the model. If engine = NULL, then spatial slendr models will by default use the "slim" back end, non-spatial models will use the "msprime" back end, and custom user-defined model scripts will use the "custom" engine. Setting this argument explicitly will change the back ends (where appropriate). Setting this argument for custom simulation script has no effect.
model_args: Optional (non-prior) arguments for the slendr model generating function. Setting this argument for custom simulation script has no effect.
engine_args: Optional arguments for the slendr simulation back end. Setting this argument for custom simulation script has no effect.
attempts: Maximum number of attempts to generate prior values for a valid demographic model (i.e. model which generates an output without error, default is 1000)
random_seed: Random seed to be used for simulation and (potentially) adding of mutations to a simulated tree sequence

Value

Either a tree-sequence object of the class slendr_ts when a slendr model was simulated, or a path to an output file when a custom simulation script was used.

Details

This function is useful to generate a small tree sequence to be used when developing summary statistic functions inference using demografr.